Although you might want to be careful with your placement of water on the mainland: your could join them up to make building a naval yard in them viable. As it is, they are rather redundant save as terrain obstacles.

Besides purely aesthetical purpose water does serves as terrain restriction to prevent tank abuse. Those large inland lakes also contain expansion Ore Nodes and those are a bit more harder to take down because of water. In general I place lakes to allow more of sneaky tactics using amphibious units.